ArticlePloS one2013
Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Integrative analyses of morphology, physiology, and transcriptional expression profiling reveal miRNAs involved in culm color in bamboo.Frontiers in plant science · 2022Article
- Natural Hybrid Origin of the Controversial "Species"Frontiers in plant science · 2021Article
- Bamboo Transposon Research: Current Status and Perspectives.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Reconstructing the phylogeny of new world monkeys (Current zoology · 2019Article
- Multiple model species selection for transcriptomics analysis of non-model organisms.BMC bioinformatics · 2018Article
- Whole-Genome Comparison Reveals Divergent IR Borders and Mutation Hotspots in Chloroplast Genomes of Herbaceous Bamboos (Bambusoideae: Olyreae).Molecules (Basel, Switzerland) · 2018Article
- A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions.PeerJ · 2018Article
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- Comparative Transcriptome and Chloroplast Genome Analyses of Two RelatedFrontiers in plant science · 2016Article
- Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks.Genome biology · 2015Article
- Transcriptome Sequencing of Lima Bean (Phaseolus lunatus) to Identify Putative Positive Selection in Phaseolus and Legumes.International journal of molecular sciences · 2015Article
- Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.AoB PLANTS · 2015Article
- Article
- ASTRAL: genome-scale coalescent-based species tree estimation.Bioinformatics (Oxford, England) · 2014Article
- De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae).Parasites & vectors · 2014Article
- The role of seasonal flowering responses in adaptation of grasses to temperate climates.Frontiers in plant science · 2014Review
- Identification and characterization of microRNAs in the leaf of ma bamboo (Dendrocalamus latiflorus) by deep sequencing.PloS one · 2013Article
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6 authors.
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Abstract
BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.
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